Hello all, I'm trying to run Freesurfer recon-all on a series of T1 images with pretty extreme bias field intensity inhomogeneities. Signal dropoff in the inferior-most and superior-most slices results in temporal lobe and superior cortical volume underestimation. It's related to the coil and is stereotypically present in every one of the scans so there should be a way to correct them all for bulk processing. I tried N4 bias field correction which resulted in a modest improvement but was far from perfect. I also tried adding control points and rerunning a subset of 20 of them as suggested elsewhere in the forum. Adding the control points improved the subset slightly, but estimating bias field from those subjects and applying the correction to everyone else resulted in worse segmentation overall. Can anyone suggest a method for correcting this? Thanks in advance for any advice. -David
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